Module: Bio::Ngs::FS

Defined in:
lib/bio/ngs/fs.rb

Class Method Summary collapse

Class Method Details

.cat(files, merged) ⇒ Object Also known as: merge

Write a file ‘merged’ which is the concatenation of multipes fastq.gz ‘files’ files is an array of filenames



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# File 'lib/bio/ngs/fs.rb', line 10

def cat(files, merged)
    if files.is_a? Array
      File.open(merged,'wb') do |fmerge|
        files.each do |fname|
          File.open(fname,'rb:binary') do |file|
          	while line = file.gets
          		fmerge << line
          	end
          end #read
        end #each
      end #write
    end #if
end

.files(everything, suffix = nil) ⇒ Object 



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# File 'lib/bio/ngs/fs.rb', line 26

def files(everything, suffix=nil)
  if everything.is_a? String
    if File.file? everything
      [File.expand_path(everything)]
    elsif File.directory? everything
        files(Dir.glob(File.join(everything, suffix.nil? ? "*" : "*"+suffix)).select{|item| File.file? item}).flatten
    elsif everything=~/\*/
      files(Dir.glob(everything)).flatten
    elsif everything=~/[ ,:;]/
     files(everything.split(/[ ,:;]/))
    end
  elsif everything.is_a? Array
    everything.map do |item|
      files(item)
    end.flatten
  end
end